Dear Amber users,
I have a system that contains DNA + ions + water. I want to calculate
hydrogen bonding between water and water, around ions within 5angtrom.
These ions are 10angstrom far away from the nucleic acid. Here are the
following commands I m not getting hydrogen bonds.
parm dna-cu.prmtop
trajin auto-0.15M-mg2+-prod1000ns.nc 1 1
reference auto-0.15M-mg2+-prod1000ns.nc 1 1
strip (:1-24<:10.0) outprefix strip nobox
strip !(:MG<:5.0) outprefix strip nobox
hbond All out All1.hbvtime.dat solventdonor :WAT solventacceptor :WAT.O
avgout All.UU.avg.dat solvout All.UV.avg.dat bridgeout All.bridge.avg.dat
go
quit
ACTION OUTPUT:
HBOND: Actual memory usage is 0.000 kB
0 solute-solute hydrogen bonds.
0 solute-solvent hydrogen bonds.
0 unique solute-solvent bridging interactions.
DATASETS (4 total):
All[UU] "All[UU]" (integer), size is 0
All[UV] "All[UV]" (integer), size is 0
All[Bridge] "All[Bridge]" (integer), size is 0
All[ID] "All[ID]" (string), size is 0
DATAFILES (4 total):
All1.hbvtime.dat (Standard Data File): All[UU] All[UV] All[Bridge]
All[ID]
All.UU.avg.dat (Avg. solute-solute HBonds)
All.UV.avg.dat (Avg. solute-solvent HBonds)
All.bridge.avg.dat (Solvent bridging info)
Warning: Set 'All[UU]' contains no data.
Warning: Set 'All[UV]' contains no data.
Warning: Set 'All[Bridge]' contains no data.
Warning: Set 'All[ID]' contains no data.
Warning: File 'All1.hbvtime.dat' has no sets containing data.
*-------------------------------------------------*
*With Regards*
*Angad Sharma*
*Research Scholar*
*School of Computational & Integrative Sciences*
*Jawaharlal Nehru University*
*New Delhi 110067, (INDIA)*
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Received on Mon Aug 29 2022 - 00:30:02 PDT
